title: Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification.
abstract: Salmonella enterica serovar Typhi, the causative agent of typhoid fever, is highly clonal and genetically conserved, making isolate subtyping difficult. We describe a standardized multiplex ligation-dependent probe amplification (MLPA) genotyping scheme targeting 11 key phylogenetic markers of the S. Typhi genome. The MLPA method demonstrated 90% concordance with single nucleotide polymorphism (SNP) typing, the gold standard for S. Typhi genotyping, and had the ability to identify isolates of the H58 haplotype, which is associated with resistance to multiple antimicrobials. Additionally, the assay permitted the detection of fluoroquinolone resistance-associated mutations in the DNA gyrase-encoding gene gyrA and the topoisomerase gene parC with a sensitivity of 100%. The MLPA methodology is simple and reliable, providing phylogenetically and phenotypically relevant genotyping information. This MLPA scheme offers a more-sensitive and interpretable alternative to the nonphylogenetic subgrouping methodologies that are currently used in reference and research laboratories in areas where typhoid is endemic.
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
authors.forename: Duy
authors.initials: D
authors.lastname: Pham Thanh
authors.forename: Nga
authors.initials: N
authors.lastname: Tran Vu Thieu
authors.forename: Chau
authors.initials: C
authors.lastname: Tran Thuy
authors.forename: Martin
authors.initials: M
authors.lastname: Lodén
authors.forename: Kiki
authors.initials: K
authors.lastname: Tuin
authors.forename: James I
authors.initials: JI
authors.lastname: Campbell
authors.forename: Nguyen
authors.initials: N
authors.lastname: Van Minh Hoang
authors.forename: Phat
authors.initials: P
authors.lastname: Voong Vinh
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Farrar
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
mesh_terms: D024881:Drug Resistance, Bacterial; D005798:Genes, Bacterial; D005838:Genotype; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic; D012485:Salmonella typhi / Q000145:classification* / Q000235:genetics*; D012680:Sensitivity and Specificity; D013997:Time Factors